Mercurial > repos > florianbegusch > qiime2_suite
diff qiime2/qiime_feature-table_merge.xml @ 14:a0a8d77a991c draft
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author | florianbegusch |
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date | Thu, 03 Sep 2020 09:51:29 +0000 |
parents | f190567fe3f6 |
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--- a/qiime2/qiime_feature-table_merge.xml Thu Sep 03 09:46:00 2020 +0000 +++ b/qiime2/qiime_feature-table_merge.xml Thu Sep 03 09:51:29 2020 +0000 @@ -1,51 +1,59 @@ <?xml version="1.0" ?> -<tool id="qiime_feature-table_merge" name="qiime feature-table merge" version="2019.7"> - <description> - Combine multiple tables</description> - <requirements> - <requirement type="package" version="2019.7">qiime2</requirement> - </requirements> - <command><![CDATA[ +<tool id="qiime_feature-table_merge" name="qiime feature-table merge" + version="2020.8"> + <description>Combine multiple tables</description> + <requirements> + <requirement type="package" version="2020.8">qiime2</requirement> + </requirements> + <command><![CDATA[ qiime feature-table merge - -#if $input_files_itables: -#def list_dict_to_string(list_dict): - #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') - #for d in list_dict[1:]: - #set $file_list = $file_list + ' --i-tables=' + d['additional_input'].__getattr__('file_name') - #end for - #return $file_list -#end def - --i-tables=$list_dict_to_string($input_files_itables) -#end if - +# if $input_files_itables: + # def list_dict_to_string(list_dict): + # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') + # for d in list_dict[1:]: + # set $file_list = $file_list + ' --i-tables=' + d['additional_input'].__getattr__('file_name') + # end for + # return $file_list + # end def +--i-tables=$list_dict_to_string($input_files_itables) +# end if #if str($poverlapmethod) != 'None': - --p-overlap-method=$poverlapmethod +--p-overlap-method=$poverlapmethod #end if +--o-merged-table=omergedtable ---o-merged-table=omergedtable +#if str($examples) != 'None': +--examples=$examples +#end if + ; cp omergedtable.qza $omergedtable - ]]></command> - <inputs> - <repeat name="input_files_itables" optional="False" title="--i-tables"> - <param format="qza,no_unzip.zip" label="--i-tables: PATH List[FeatureTable[Frequency]] The collection of feature tables to be merged. [required]" name="additional_input" type="data"/> - </repeat> - <param label="--p-overlap-method: " name="poverlapmethod" optional="True" type="select"> - <option selected="True" value="None">Selection is Optional</option> - <option value="error_on_overlapping_sample">error_on_overlapping_sample</option> - <option value="error_on_overlapping_feature">error_on_overlapping_feature</option> - <option value="sum">sum</option> - </param> - </inputs> - <outputs> - <data format="qza" label="${tool.name} on ${on_string}: mergedtable.qza" name="omergedtable"/> - </outputs> - <help><![CDATA[ + ]]></command> + <inputs> + <repeat name="input_files_itables" optional="False" title="--i-tables"> + <param format="qza,no_unzip.zip" label="--i-tables: ARTIFACTS... List[FeatureTable[Frequency]] The collection of feature tables to be merged. [required]" name="additional_input" optional="False" type="data" /> + </repeat> + <param label="--p-overlap-method: " name="poverlapmethod" optional="True" type="select"> + <option selected="True" value="None">Selection is Optional</option> + <option value="error_on_overlapping_sample">error_on_overlapping_sample</option> + <option value="error_on_overlapping_feature">error_on_overlapping_feature</option> + <option value="sum">sum</option> + </param> + <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" /> + + </inputs> + + <outputs> + <data format="qza" label="${tool.name} on ${on_string}: mergedtable.qza" name="omergedtable" /> + + </outputs> + + <help><![CDATA[ Combine multiple tables -####################### +############################################################### Combines feature tables using the `overlap_method` provided. @@ -60,9 +68,9 @@ ------- merged_table : FeatureTable[Frequency] The resulting merged feature table. - ]]></help> -<macros> + ]]></help> + <macros> <import>qiime_citation.xml</import> -</macros> -<expand macro="qiime_citation"/> -</tool> + </macros> + <expand macro="qiime_citation"/> +</tool> \ No newline at end of file